With regards to the grading system, they compare your KDA, CS, etc.. with everyone else who plays that champ in that role. When your score is in a certain percentage, it gets that grade. So, if the average katarina player goes 5/5/5, getting that score would get you like a C. If the top 1% gets 10/0/0 or higher, then you have to exceed that score to get an S. I'm making up these numbers, as no one has the exact ones, but it's just to illustrate the point.
This means lower usage champs have less of a sample size, and therefore less people who are 'masters' at it.. i.e. the bar is lower.
I've seen someone get an S+ with like an 11/5/8 score, while someone in the same game got an A- for a 12-2-9 score, and similar CS numbers.
As for the mastery/rune question,
zombiewizardhawk
If any of the talent points are for crits.. some people just want 1% crit chance for the occasional lucky crit in early laning. There is a large difference between 0 and 1%, but less of a difference then 1 to 2%. Or, they just want a few % of lifesteal for some sustain, but not the full amount from that mastery. With some masteries, the first point over 0 can be a big difference, but it has slightly diminishing returns and is not quite as worth for putting more points. With the example you mentioned, you might want a tiny bit of lifesteal for slow regen while laning, but you want the late game damage from the other mastery. A 1/4 split could make sense then. Especially on a hybrid champ that gets full benefit from that other mastery.
With rune pages, some times you want like 5% CDR at lvl 18 (because your build gets 35%), or a certain amount of CDR reduces a specific ability by enough that you can pull off combos you couldn't otherwise. Like, with 10% cdr, your Q is back up by the time you cast W and E for a burst combo. That's one of the reason you sometimes see weird rune setups with a weird number of CDR at lvl 18 runes, or just a single crit rune, etc..